- BBClist - maillist.psb.ugent.be

PhD position in bioinformatics, genomics and network analysis in Marseille
by Anaïs BAUDOT 25 Jan '19

25 Jan '19

Dear colleagues, We are proposing a PhD position related to the bioinformatic analysis of common and Mendelian diseases. The objective of this PhD project is to investigate the shared architecture between Mendelian and common diseases both at the phenotypic and molecular levels by identifying subnetworks enriched in mutations and variations. As a consequence, this approach will also help predicting the relevant variations (SNPs, eQTLs) implicated in common polygenic diseases, or acting as modifier to modulate Mendelian diseases. Details of the project and host labs can be found here: http://centuri-livingsystems.org/phd2018-12/ <http://centuri-livingsystems.org/phd2018-12/> This PhD project is part of the PhD Programme of the Turing Centre for Living Systems (CENTURI). The deadline of application is: February 15, 2019 and the application procedures is explained here: http://centuri-livingsystems.org/recruitment <http://centuri-livingsystems.org/recruitment> The PhD student should have a Master’s degree in an area related to Bioinformatics, Computer Science or Mathematics with interest for data analysis, graph theory and human genetics. Sincerely, Aitor Gonzalez & Anaïs Baudot -------------------------------------------------- Aitor GONZÁLEZ Aix-Marseille Université UMR1090 TAGC 163, avenue de Luminy - case 928 13288 Marseille cedex 09 Tel +33 (0)491 82 87 48 <tel:+33%20491%2082%2087%2048> Fax +33 (0)491 82 87 01 <tel:+33%20491%2082%2087%2001> http://www.aitorgonzalezlab.org/ <http://www.aitorgonzalezlab.org/> --------------------------------------------------------- Anaïs BAUDOT MMG, Marseille Medical Genetics U 1251, Faculté de Médecine de La Timone, 27 Bd Jean Moulin 13385 Marseille Cedex 5 0491324948 France https://www.marseille-medical-genetics.org/a-baudot/ anais.baudot(a)univ-amu.fr

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Vacancies @ELIXIR Belgium
by Kim DE RUYCK 25 Jan '19

25 Jan '19

Dear, ELIXIR Belgium is looking for talented people to join current multidisciplinary team . If you’re interested in contributing to building the data research infrastructure for the future for life-sciences, one of these positions could be your next professional challenge. * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Data Steward ] * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Scientific Cloud Coordinator ] * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Open Science Community Manager ] * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Bioinformatics Trainer ] * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Software developer cloud data processing ] * [ https://elixir-belgium.us14.list-manage.com/track/click?u=d1bc1ab5d122d661a… | Software developer data management tools ] Kind regards, Kim De Ruyck Kim De Ruyck PhD Coordinator ELIXIR Belgium VIB, Technologiepark 71, 9052 Gent | +32 (0)9 33 13 694 [ http://www.elixir-belgium.org/ | www.elixir-belgium.org ] [ https://twitter.com/ELIXIRnodeBE | @ELIXIRnodeBE ] [ http://eepurl.com/cl-xOX | Subscribe to our mailing list ]

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PhD position in Bioinformatics on biomarker development for dementias
by Sanne Abeln 23 Jan '19

23 Jan '19

Dear students & colleagues, We seek a new colleague who will work on a collaborative PhD project between the Neurochemistry group at the Alzheimer Center Amsterdam UMC-locations VUmc and Bioinformatics at the Vrije Universiteit Amsterdam. The aim is to develop novel approaches in biomarker development for dementias. Crucial is here to develop models to rationalise the prediction how biomarkers, in a specific medium, will be able to bind specific antibodies for detection. Therefore, bioinformatics and structural bioinformatics will play an important role in this PhD project. *The application deadline is 7 Februari 2019*. Please see the link below for further details and how to apply: https://werkenbij.vu.nl/ad/phd-position-in-bioinformatics/f1cnnr It would be nice if you could share this position with potential candidates, Kind regards, Sanne -- Sanne Abeln Associate Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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Invitation to submit your abstract to Training, Education and Capacity Building Session at BioSB conference. Deadline January 25, 2019
by Celia van Gelder 19 Jan '19

19 Jan '19

* Apologies for cross-posting - Dear colleague, We are happy to announce that this year on the BioSB conference ( <https://www.aanmelder.nl/biosb2019/abstract-submission> 2-3 April 2019 in Lunteren) there will be a session devoted to Training, Education & Capacity building. This session can only take place if there are enough high-quality submissions related to these topics, so your input is more than welcome!! With this mail we want to invite you to submit an abstract related to your work in training, education, skill building etc. It can be an abstract for an oral presentation (deadline January 25 2019), but also for a poster (deadline March 15, 2019). Possible topics would include, but are not limited to: - experiences in interdisciplinary/bioinformatics/data-science teaching - evaluation of best practices in training, and how to exchange them - increase of computer science/maths/data-science components in bio/medical and other bachelor and/or master curricula - how to shape the bioinformatics/life-sciences-data-science teaching landscape in NL - curriculum building for specific areas, e.g. Open Science, Data Stewardship etc. - how to evaluate the impact of training activities - train the trainer activities - training gap analysis We are looking forward to your submissions and hope to see you in Lunteren in April! Best regards Celia van Gelder, BioSB Conference Education & Training Session Chair Anton Feenstra, BioSB Conference Programme Committee Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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Winter Class 2019 on "T-cell dynamics
by Deutekom, E.S. (Eva) 18 Jan '19

18 Jan '19

Dear all, There will be a Winter Class 2019 on "T-cell dynamics" on 11th and 12th March 2019 at the Centre for Complex System Studies in Utrecht the Netherlands. You find more information about it on our webpage w<http://www.tcell-2019.eu/>ww.tcell-2019.eu<http://www.tcell-2019.eu/>. The webpage is also the place to go if you would like to register for this Winter Class. Attached you will find the poster, feel free to spread the news and to help us advertising. Kind regards, -- Eva S. Deutekom, MSc. Theoretical Biology and Bioinformatics | Department of Biology | Faculty of Science | Utrecht University Z531 | Padualaan 8 | 3584 CH Utrecht | The Netherlands

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Course Single cell RNA-seq data analysis with Chipster, Espoo, Finland, 14-15 March 2019
by Celia van Gelder 18 Jan '19

18 Jan '19

On behalf of Eija Korpelainen (CSC/ELIXR-FI) Applications are open until 25.1.2019 for the ELIXIR-FI course "Single cell RNA-seq data analysis with Chipster" which takes place in Espoo, Finland 14.-15.3.2019. <https://www.csc.fi/web/training/-/bioweek-single-cell-chipster-2019> https://www.csc.fi/web/training/-/bioweek-single-cell-chipster-2019 Best Celia Dr. Celia W.G. van Gelder Programme Manager DTL Learning Training Coordinator ELIXIR-NL ELIXIR Training Platform Leader tel. +31613375327 e-mail: <mailto:celia.van.gelder@dtls.nl> celia.van.gelder(a)dtls.nl websites: <http://www.dtls.nl/> www.dtls.nl, <http://www.biosb.nl/> www.biosb.nl skype: celia.van.gelder Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht Postal address: Postbus 8500 | 3503 RM Utrecht While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.

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CarpentryConnect Manchester 2019 Call for Proposals
by Mateusz Kuzak 17 Jan '19

17 Jan '19

On behalf of Alexandra > Dear All, > > The first European CarpentryConnect event will be held in Manchester, UK, on 25-27 June 2019 under the theme "Training Communities: Challenges and Opportunities in Europe" with an aim to, once again, bring the Carpentry community together. > > We are delighted to open the call for topic suggestions and abstract submissions for breakout sessions (group discussions such as “Carpentry Methods in University Courses”, “Diversity and Inclusion”, “Sustainable Software Practices”), workshops (longer sessions or training on specific topics such as “Ally workshop”, “Contributing on GitHub”, “Project Leadership”, “Shell Tips and Tricks”), lightning talks and posters under the following general themes: > > • > Lesson/curricula development (e.g. working on existing curricula or establishing completely novel materials, new introductory or intermediate lessons) > • > Increasing the sustainability of scientific software and research through training > • > Good teaching practices in research computing (e.g. different approaches for different levels of lesson, different workshop formats) > • > Tools and resources for teaching computational methods to researchers > • > Other topics relating to The Carpentries community or delivering training in research software: > > • > Building a local carpentry group/community at research institutions > • > Running a Carpentry membership at an institution > • > Bringing the Carpentries curriculum to universities > • > Attracting funding or making a case with the senior management for workshops/membership at your institution > > > > We strongly encourage contributions from new members of the Carpentries community, with or without any experience of running a session at a conference. > > A draft programme for the conference is available online. > > You can submit an abstract or your suggestions using the submission form until 1 March 2019. The notification of the outcome of your application will be sent out by 1 April 2019. > > Looking forward to seeing you in Manchester in June! > > Best wishes for 2019, > The CarpentryConnect Manchester 2019 Programme Subcommittee > The Carpentries / discuss / see discussions + participants + delivery options Permalink

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Cytometry Part A special issue on Machine Learning for Single-Cell Analysis
by Yvan Saeys 14 Jan '19

14 Jan '19

Dear colleagues, Please findattached a call for papers for a special issue of Cytometry Part A on Machine learning for single-cell analysis that I am editing together with Greg Finak. If you know of any interested colleagues, please forward further. Best regards, Yvan -- =============================================================================== Prof. dr. Yvan Saeys VIB Group Leader Data mining and modeling for biomedicine UGent Department of Applied Mathematics, Computer Science and Statistics Krijgslaan 281, S9, B-9000 Gent VIB-UGent Center for Inflammation Research Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium Tel : +32(0)9 331 37 40 Fax : +32(0)9 221 76 73 Mailto: yvan.saeys(a)ugent.be http://www.dambi.ugent.be ===============================================================================

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Save the date: Boost Your Visibility - Improving F of FAIR for Dutch Training and Data Resources through Bioschemas, Hackathon, 7-8 February 2019, Utrecht, the Netherlands
by Mateusz Kuzak 10 Jan '19

10 Jan '19

-- apologies for cross posting -- Dear colleague, Are you a training provider/organizer with a catalogue of training events and/or training materials or a data provider, curator or manager of Life Science resources such as Biobanks, Proteins, Samples, Beacons, Tools? Then this hackathon may be very relevant for you! DTL and ELIXIR-NL are organising a workshop/hackathon for content providers of Life Science resources such as Proteins, Samples, Beacons, Tools, and Training events and materials. Join this event to learn how to make your resources rank higher on (Google, Bing, Yahoo and other) search result pages or include your resource in relevant registries (like TeSS, the ELIXIR Training Portal) and receive more web traffic can raise the exposure of your work to be found by larger audiences. The event will start at lunch time on Thursday February 7 and will finish on Friday February 8 at 4pm. In the first half day of this 1.5 day event participants will learn about schema.org and bioschemas from experts working on Bioschemas definitions and implementations for ELIXIR resources and they will get some examples of successful Bioschemas implementations in Life Science resources, both from within and outside the Netherlands. The second day will have the form of a hackathon during which participants will work on adding Bioschemas metadata to their resources with the help of the experts. For training materials and events we will also add them to the ELIXIR’s Training Portal TeSS. Please find more information and the draft agenda here and mark the dates in your agenda if you are interested. The registration will open at the beginning of January. Looking forward to seeing you at the hackathon! On behalf of DTL/ELIXIR-NL, Celia van Gelder and Mateusz Kuzak — Mateusz Kuzak Scientific Community Manager | Dutch Techcentre for Life Sciences e-mail: mateusz.kuzak(a)dtls.nl | tel. +31 643707254 twitter: @matkuzak | github: mkuzak | skype: mkuzak Visting address: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw Jaarbeursplein 6 | 3521 AL Utrecht

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PhD position in Medical Genetics, VUB
by Matthieu Defrance 09 Jan '19

09 Jan '19

PhD Position: Integromics (genomics, transcriptomics, epigenomics) data analysis & applied bioinformatics in rare genetic diseases like cardiac arrhythmias and neurodevelopmental disorders Location: Centre for Medical Genetics Vrije Universiteit Brussel (Faculty of Medicine and Pharmacy) Contact: Sonia Van Dooren (Sonia.VanDooren(a)uzbrussel.be) Starting date: as soon as possible Context: Doctoral research concerning the added value of integrated versus single multi-omics (whole genomics, transcriptomics, epigenomics) data analysis in the context of the Innoviris BRIDGE project IGenCare ‘Integrated Medical Genomics Care Solution for Patients with Rare Genetic Diseases’ in a collaboration between VUB, ULB, BRIGHTcore (http://www.brightcore.be/) and (IB)2 (http://ibsquare.be/) Some background: In the era of high-throughput massive parallel sequencing, genome-wide analyses have become standard in medical health care. Although this (r)evolutionary technology has been increasingly important in the improvement of the genetic diagnostic yield in patients with rare genetic diseases, scientists and health care providers still phase many challenges. Indeed from the laboratory point of view, scientists had to limit most of the diagnostic genomic analyses to partial analysis of the human genome for cost-effectiveness reasons. This has on the one hand led to a higher number of genetic diagnoses, but on the other hand also to a higher number of unsolved cases, due to lack of identification of potentially causal variants and/or due to uncertainty in interpretation of the data. The project: With the implementation of low cost whole human genome sequencing, transcriptomics and epigenomics we enter a novel time frame of functional genomics and integromics health care, further expanding the possibilities in identifying the cause of rare genetic diseases. Part of the IGenCare project focuses at the laboratory level, where we plan to extend the diagnostic yield of rare genetic diseases by a multi-omics / functional genomics / integromics approach through simultaneous analysis of the patient’s whole genome, gene expression and epigenetic regulation profile in an integrative way. The tasks: - Support in the massive parallel sequencing & array multi-omics data generation through NovaSeq6000, HiSeq1500 & Iscan in collaboration with the BRIGHTcore team - Analysis of the multi-omics data and genotype-phenotype correlation at the single omics level - Evaluation and validation of the multi-omics data interpretation bioinformatics tool and GUI in collaboration with the (IB)2 multi-omics data integrator team - Support in the optimization of multi-omics integrator pipelines, algorithms and annotation tools - Implementation and application of the multi-omics integrator tool Continuous communication in a constant feedback loop between the multi-omics integrator tool and GUI developers on the one hand and the omics data interpretation experts on the other hand You are a bioengineer or a master in computational, biomedical or life sciences, with a strong affinity for applied bioinformatics and multi-omics data analysis. Requirements: You have knowledge of: - Multi-omics (full genome, transcriptome & epigenome) technology - Bioinformatics in a next generation sequencing and array workbench environment (data assembly, analysis and annotation) You are competent in: - Computational aspects of genomics, transcriptomics and / or epigenomics - Scripting and / or programming (eg R, Perl, Linux, Python, C, ...) - Relational databases (MySQL, PostgreSQL) You have capacities in: - Problem-solving (thinking & acting) - Fluent communication (oral & written) - Multi-tasking - Taking initiative, working autonomously - Positive attitude and team work - Eagerness to learn and you are driven to contribute to innovative research and diagnostics You are fluent in languages: - Excellent knowledge of the English language (oral & written) - Some knowledge of Dutch is desirable but not essential

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